comparison blupcal.xml @ 1:c1c85170db1b draft default tip

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0:45d215f2be74

<tool id="blup_and_blue_multiple2" name="BLUP/BLUE" version="1.11.0">
  <description>calculator (multiple traits)</description>
  <requirements>
  <requirement type="package" version="1.1_18_1">r-lme4</requirement> 
  <requirement type="package" version="1.20.2">r-getopt</requirement>
  </requirements> 
  <command interpreter="bash">
./blupcal.sh $__tool_directory__ $galaxy_tabular_file $galaxy_replication_vector_column_index $galaxy_genotype_vector_column_index $galaxy_first_y_vector_column_index $galaxy_last_y_vector_column_index $galaxy_design_conditional.galaxy_design 
 $galaxy_summarize_by
 $galaxy_summarize_by_vector_column_index

</assert_contents>
</output>
  </test>
  </tests>
  <help>
**What it does**

This function calculates BLUP, BLUE and means for Y variable based on the model specified by the user.

The required variables for RCBD are Genotype and Replication and for lattice required variables are Genotype, Replication (main block) and Block within Replication (sub block or block). User can add additional two X variables (eg. Location, Season etc) in the model and are treated as factor ( even supplied as numerical variable).

- Genotype is treated as Fixed for BLUE calculation and random for BLUP calculation.
- Replication, Block within Replication are treated as random both BLUP and BLUE calculations.
- Variable 1, Genotype : Variable 1  are treated as random both BLUP and BLUE calculations.
- Variable 2, Genotype : Variable 2, Variable 1 : Variable 2, Genotype : Variable 1 : Variable 2  are treated as random effects for both BLUP and BLUE calculations.


**Citation**
Douglas Bates, Martin Maechler, Ben Bolker, Steve Walker (2015). Fitting Linear Mixed-Effects Models Using lme4. Journal of Statistical Software, 67(1), 1-48.

**Author(s)**
  </help>
</tool>

1:c1c85170db1b

<tool id="blup_and_blue_multiple2" name="BLUP/BLUE" version="1.11.0">
  <description>calculator (multiple traits)</description>
  <requirements>
  <requirement type="package" version="1.1_18_1">r-lme4</requirement> 
  <requirement type="package" version="1.20.2">r-getopt</requirement>
  <requirement type="package" version="1.10_1">r-arm</requirement>
  </requirements> 
  <command interpreter="bash">
./blupcal.sh $__tool_directory__ $galaxy_tabular_file $galaxy_replication_vector_column_index $galaxy_genotype_vector_column_index $galaxy_first_y_vector_column_index $galaxy_last_y_vector_column_index $galaxy_design_conditional.galaxy_design 
 $galaxy_summarize_by
 $galaxy_summarize_by_vector_column_index

</assert_contents>
</output>
  </test>
  </tests>
  <help>

.. class:: infomark 

**BLUP/BLUE calculator, based on lme4 R package version 1.1_18_1**

.. class:: infomark 

**Galaxy integration** Provided by EiB platform and GOBii and Angel Villahoz-Baleta (Cornell Univ)

.. class:: infomark

**Integration contributors**  Juan David Arbelaez Velez (IRRI), Dereeper Alexis, Juan Burgueno (CIMMYT)

.. class:: infomark 

**Support** For any questions about this tool, please send an e-mail to [e-mail]



**What it does**

This function calculates BLUP, BLUE and means for Y variable based on the model specified by the user.

The required variables for RCBD are Genotype and Replication and for lattice required variables are Genotype, Replication (main block) and Block within Replication (sub block or block). User can add additional two X variables (eg. Location, Season etc) in the model and are treated as factor ( even supplied as numerical variable).

- Genotype is treated as Fixed for BLUE calculation and random for BLUP calculation.
- Replication, Block within Replication are treated as random both BLUP and BLUE calculations.
- Variable 1, Genotype : Variable 1  are treated as random both BLUP and BLUE calculations.
- Variable 2, Genotype : Variable 2, Variable 1 : Variable 2, Genotype : Variable 1 : Variable 2  are treated as random effects for both BLUP and BLUE calculations.

  </help>
  <citations>
         <citation type="doi">10.18637/jss.v067.i01</citation> 
  </citations> 
</tool>